Table 1

Overrepresentation of MIPS functional categories in genes that were differentially transcribed in response to fully fermentative conditions. Clusters A&B, 2 & 3 and 4, 5 & 6 had similar expression pattern and similar enrichments, and were therefore pooled before the overrepresentation analysis. Enrichment was estimated by hypergeometric distribution analysis (cut-offs around 10^-5, see Materials and Methods); magnitude of the enrichment is indicated by the p-value.
MIPS_cat.			A&B (283 genes)		C (237 genes)		D (87 genes)

nr.	description	nr of genes^a	nr of genes^b	p-value	nr of genes^b	p-value	nr of genes^b	p-value

01	METABOLISM	1531					38	3.8E-05
01.01	amino acid metabolism	243	28	2.6E-06	29	1.7E-08
01.01.06	metabolism of the aspartate family	64			13	4.5E-07
01.01.06.05.01	biosynthesis of methionine	14			5	1.0E-04
01.03	nucleotide metabolism	230	23	6.3E-05	23	1.2E-05
01.03.01	purine nucleotide metabolism	66			17	3.8E-09
01.03.01.03	purine nucleotide anabolism	29			13	7.4E-12
01.05.01	C-compound and carbohydrate utilization	510					18	1.4E-04
01.05.01.07.03	tetrahydrofolate-dependent C-1-transfer	14			6	5.8E-06

11	TRANSCRIPTION	1036	126	9.4E-31
11.02.01	rRNA synthesis	56	12	4.4E-06
11.02.02	tRNA synthesis	39	9	3.8E-05
11.04	RNA processing	394	89	9.4E-42
11.04.01	rRNA processing	174	78	8.7E-62
11.06	RNA modification	65	19	2.1E-11
11.06.01	rRNA modification	17	9	1.0E-08

12	PROTEIN SYNTHESIS	511	63	1.7E-14	103	7.6E-53
12.01	ribosome biogenesis	343	49	8.5E-14	89	1.0E-54
12.01.01	ribosomal proteins	277			88	1.8E-62

14	PROTEIN FATE (folding, modification, destination)
14.07.02	modification with sugar residues	70					8	4.1E-06
14.07.02.01	O-directed glycosylation	16					4	5.2E-05

16	PROTEIN WITH BINDING FUNCTION	1049	82	4.6E-08
16.03	nucleic acid binding	346	47	2.0E-12
16.03.03	RNA binding	194	31	2.8E-10

20	CELLULAR TRANSPORT, TRANSPORT FACILITATION...	1038
20.01.13	lipid transport	43					5	3.3E-05
MIPS_cat.			1 (120 genes)		2 & 3 (577 genes)		4, 5 & 6 (617 genes)

nr.	description	nr of genes^a	nr of genes^b	p-value	nr of genes^b	p-value	nr of genes^b	p-value

01	METABOLISM	1531			193	4.3E-08	192	1.3E-05
01.05	C-compound and carbohydrate metabolism	510			89	2.6E-10	80	4.9E-06
01.05.01.01.01	sugar, glucoside, polyol and carboxylate catabolism	82					27	4.7E-09
01.06	lipid, fatty acid and isoprenoid metabolism	292					55	6.6E-07
01.06.01.07	isoprenoid metabolism	41					14	1.6E-05
01.06.01.07.11	tetracyclic and pentacyclic triterpenes biosynthesis	36					13	1.6E-05

02	ENERGY	360			112	5.1E-35	69	1.1E-08
02.10	tricarboxylic-acid pathway	31			11	4.7E-05	12	1.5E-05
02.11	electron transport & membrane-ass. energy conservation	54			30	4.2E-18
02.13	Respiration	131			53	1.1E-22
02.13.03	aerobic respiration	74			38	5.2E-21
02.19	metabolism of energy reserves	53					16	2.4E-05
02.25	oxidation of fatty acids	9			6	3.5E-05
02.45.15	energy generation (e.g. ATP synthase)	18					9	1.5E-05

11	TRANSCRIPTION
11.02.03.04.01	transcriptional activator	42	7	1.2E-05

14	PROTEIN FATE (folding, modific., destination)	1167					173	1.6E-08
14.07.11	protein processing (proteolytic)	92					24	4.1E-07
14.13	protein degradation	264					61	3.6E-11
14.13.01	cytoplasmic and nuclear protein degradation	194					48	4.2E-10
14.13.01.01	proteasomal degradation	134					33	2.8E-07

20	CELLULAR TRANSPORT, TRANSPORT FAC.	1028
20.01.15	electron/hydrogen transport	76			24	2.3E-08
20.09	transport routes	695					98	4.2E-05

32	CELL RESCUE, DEFENSE AND VIRULENCE	559			77	7.4E-05
32.01	stress response	454			73	4.2E-07
32.01.01	oxydative stress response	56			18	10E-06
32.01.07	unfolded protein response (ER quality control)	74			16	7.6E-04

42	BIOGENESIS OF CELL. COMPONENTS
42.16	mitochondrion	170			38	9.0E-08	35	1.1E-05

a: amount of genes in the genome belonging to the specified functional category b: amount of genes in the respective clusters or group of clusters belonging to the specified functional category
van den Brink et al. BMC Genomics 2008 9:100 doi:10.1186/1471-2164-9-100